This document summarizes a metagenomics and zoonotic pathogen discovery platform. It developed highly multiplexed sequencing techniques that reduced costs. Using samples from wildlife, livestock, humans and vectors, it identified several viruses in East Africa, including Rift Valley Fever virus, and developed diagnostic tools. Over 250 pathogen sequences were submitted to gene banks. The platform aims to enhance disease surveillance and control in Africa through early detection, which can reduce animal losses and improve food security, health and incomes. Future work includes expanded surveillance, utilizing developed diagnostic tools, and new collaborations.

1. Pathogen discovery platform
George N. Michuki
ILRI BioSciences Day, Nairobi, 27 November 2013

2. Metagenomics and zoonotic pathogen
discovery platform
• Introduction
• Enabling livestock health and disease surveillance
• Outbreaks detection  control  preventing animal loss
• Outcomes useful to:
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Scientists and veterinarians
Health professionals
Policy makers
Farmers and livestock handlers
• Impacts of project:
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Diagnostic tools and vaccine development
Prevalent human zoonotic diseases
Appropriate control measures (human and animals)
Risks exposed to and control measures

3. The problem: its significance
• Increase of emergence and re-emergence of zoonotic
infectious diseases in Africa in the past years
• Recent outbreaks of viral diseases include:
• Yellow Fever, Dengue, Rift Valley Fever, Onyongnyong, Crimean Congo Hemorrhagic Fever and Chikungunya
viruses
• Studies revealed that livestock and wildlife are involved in
the spread of these diseases and are also affected
• Animal diseases control impacts on: Improved food security (SLO2)
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Animal production as food source
Trade (No sanctions)
Income source (Animal sale)
Zoonotic disease control
Improved nutrition and
health (SLO3)

4. Methods
• Analysis of samples from diverse sources
• Wildlife, domestic animals, human and vectors
• Analysis of diverse sample types
• Tissue, blood, serum, swabs and cultures
• Use of next generation sequencing and RT-PCR
• Metagenomic approach
• Targeted amplicon sequencing
• High resolution melt analysis
• Collaborating partners
• Local: KWS, DVS, ICIPE, KEMRI, KARI,
• International: Makerere
University, OVI, CSIRO, LANL

5. Results-1
• Highly multiplexing techniques developed
• Reduced cost of sequencing
• Universal 16S and 18S tools developed
• Enables simultaneous identification of vector and
associated fungi and bacteria
• Internal Local database and Genebank:
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Dugbe virus,
Semliki Forest virus,
Bunyamwera virus,
Partial Rift Valley Fever virus
Babanki virus
West Nile Virus
Ndumu viruses
Developed Mosquito typing tools
Impact on animal
and human health

6. Results-2
• In collaboration with partners:
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ECF vaccine quality check - ILRI
Equine Encephalosis Virus – (OVI – South Africa)
Blue Tongue Virus (OVI – South Africa)
RVF viruses (OVI – South Africa)
New Castle Disease Virus – ILRI – in Genebank
Pigeon Paramyxovirus Virus –KWS – in Genebank
o Velogenic – fusion gene motif similar to chicken outbreak NDV
o Plasmodium falciparum – Kilifi welcome trust
o MHC class 1 and 2 – ILRI vaccine group
o Chikungunya Viruses – in genebank and paper submitted
o Identified a single mutation affecting replication rate
o Ndumu virus from pigs: - in genebank
• Over 250 sequences in genebank
• Several publications in the pipeline

7. Conclusions and discussion points
• Developed Mosquito typing tools
• Useful for typing vectors involved in disease transmission
• Early detection of disease by vector identification
• Pigeon Paramyxovirus Virus (NDV)
• Virulent determinant gene segment identified
• Similar to strains causing outbreaks in chicken
• Quick detection of outbreaks in chicken
• Wide range of viral pathogens identified
• Development of a multiplex screening diagnostic tool
• What are the next challenges?
• Mapping of the disease patterns
• Vaccine and treatment options
• NEW RESEARCH OPPORTUNITIES

8. Where to from now?
• Increased surveillance coverage and larger scale of pathogen
discovery
• Utilization of developed tools
• Decreased animal losses by early detection:
• Increase income reducing poverty
• Animal disease management will increase production thus improving on
food security.
• Control of zoonotic diseases will improve on health of farmers.
• New and enforcing existing collaboration
• New: LANL and DTRA
• Existing: DVS, KWS, ICIPE, KEMRI

9. General discussion (facultative)
• Enhancing situational awareness of emerging viral disease threats
in East Africa
• Proposal submitted to DTRA
• At the 2nd stage (white paper submitted)

10. better lives through livestock
ilri.org
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